Protocol 4 - Provenance data with shipwrecks
The following example applies protocol 4 to confirm shipwrecks samples attribution to workshops’ provenance groups.
Protocol 4 consist in:
- Select provenance-specific variables in geochemical compositional data (CoDa) and ordinal petrographic data;
- Centred log-ratio transformation (clr) and transform to ranks;
- Extended Gower coefficient of dissimilarity, using Relative ranking difference (RRD);
- Apply Principal Coordinates Analysis (PCoA);
- Perform PERMANOVA & PERMDISP tests;
Last, search for outliers and re-do protocol excluding outliers.
NOTE: The initial procedures must be ran at least once before any protocol can be applied.
Ordination procedure
As protocol 3, protocol 4 performs PCoA on a distance matrix calculated with Extended Gower coefficient of dissimilarity, combining Euclidean distances on transformed compositional data (50%) and RRD on ranked petrographic data (50%). In this case, we are not filtering out the shipwreck samples, but we do exclude the true outliers (IND, observations with no group assigned) so they don’t pollute visualization.
prot4_Shipwreck_2d <- apply_ordination(# no true outliers
cleanAmphorae[!isTrueIND,],
"4", # select protocol 4
exception_columns = excep_cols,
variable_tags = varCode,
coda_override = chemVars16,
coda_transformation = "CLR")
prot4_Shipwreck_3d <- apply_ordination(# no true outliers
cleanAmphorae[!isTrueIND,],
"4", # select protocol 4
exception_columns = excep_cols,
variable_tags = varCode,
coda_override = chemVars16,
coda_transformation = "CLR",
dimensions = 3)Simplify CoDa names
We may want to simplify the names of the transformed variables before plotting them in a biplot.
prot4_Shipwreck_2d <- simplify_coda_names(prot4_Shipwreck_2d)
prot4_Shipwreck_3d <- simplify_coda_names(prot4_Shipwreck_3d)Test the given provenance groups
We can test the provenance assigned to shipwrecks’ amphorae samples together with those found and assigned to the workshops.
prot4_Shipwreck_tests <- test_groups(prot4_Shipwreck_2d$dist_matrix,
factor_list_Shipwreck$ProvGroup)
#> [1] "initiating test batch..."
#> [1] "vegan::anosim done."
#> [1] "vegan::betadisper done."
#> [1] "vegan::permutest done."
#> [1] "vegan::adonis done."
#> [1] "Test batch completed."These tests were explained in protocol 1.
Biplots
The details on how to create biplots is already explained in protocol 1. Protocol 4 generates PCoA projections.
Biplot 2D
arrows_label_adj <- rbind(c(.5,0),c(.5,1),c(.5,0),c(.5,1),c(.5,0),
c(.5,1),c(.8,0),c(1,.5),c(.5,0),c(1,.2),
c(.5,1),c(.2,.7))
row.names(arrows_label_adj) <- c("S7","S8","S4","CaO","MgO",
"S11","L48","SiO2","Ce","Nb",
"Th","TiO2")
biplot2d3d::biplot_2d(prot4_Shipwreck_2d,
ordination_method = "PCoA",
invert_coordinates = c (TRUE,TRUE),
ylim = c(-.3,.25),
point_type = "point",
groups = factor_list_Shipwreck$ProvGroup,
group_color = color_list_Shipwreck$ProvGroup,
group_label_cex = 0.6,
arrow_mim_dist = .5,
arrow_label_cex = 0.6,
arrow_fig = c(.6,.95,0,.35),
arrow_label_adj_override = arrows_label_adj,
subtitle = prot4_Shipwreck_2d$sub2D,
test_text =
prot4_Shipwreck_tests$text(prot4_Shipwreck_tests),
test_fig = c(0, 0.5, 0.62, .99),
fitAnalysis_fig = c(0,.7,.05,.5),
output_type = "preview")
protocol 4 with shipwrecks
Biplot 3D
biplot2d3d::biplot_3d(prot4_Shipwreck_3d,
ordination_method = "PCoA",
point_type = "point",
groups = factor_list_Shipwreck$FabricGroup,
group_color = color_list_Shipwreck$FabricGroup,
group_representation = "stars",
star_centroid_radius = 0,
star_label_cex = .8,
arrow_min_dist = .5,
arrow_body_length = .025,
subtitle = prot4_Shipwreck_3d$sub3D,
test_text =
prot4_Shipwreck_tests$text(prot4_Shipwreck_tests),
test_cex = 1.25,
test_fig = c(0, 0.5, 0.65, .99),
view_zoom = 0.9)
biplot2d3d::animation(directory = directories$prot4_Shipwreck,
file_name = "Prot4_Shipwreck_Biplot3D")
Prot4_Shipwreck_Biplot3D.gif